+Open data
-Basic information
Entry | Database: PDB / ID: 5j3q | ||||||
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Title | Crystal structure of S. pombe Dcp1:Edc1 mRNA decapping complex | ||||||
Components |
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Keywords | HYDROLASE / decapping / mRNA decay / EVH1 | ||||||
Function / homology | Function and homology information mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / meiotic cell cycle / P-body / cytoplasmic stress granule / mRNA processing / RNA binding ...mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / meiotic cell cycle / P-body / cytoplasmic stress granule / mRNA processing / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Valkov, E. / Muthukumar, S. / Chang, C.T. / Jonas, S. / Weichenrieder, O. / Izaurralde, E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2016 Title: Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation. Authors: Valkov, E. / Muthukumar, S. / Chang, C.T. / Jonas, S. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j3q.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j3q.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 5j3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/5j3q ftp://data.pdbj.org/pub/pdb/validation_reports/j3/5j3q | HTTPS FTP |
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-Related structure data
Related structure data | 5j3tC 5j3ySC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15294.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: dcp1, SPBC3B9.21 / Plasmid: pnEApG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: Q9P805 #2: Protein/peptide | Mass: 2742.089 Da / Num. of mol.: 2 / Fragment: UNP residues 155-180 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10108 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M PCB buffer (sodium propionate, sodium cacodylate and BIS-TRIS propane in a molar ratio of 2:1:2, (pH 6.0)), 25% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2015 / Details: DYNAMICALLY BENDABLE MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→19.54 Å / Num. obs: 24087 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.87→1.91 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 0.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J3Y, CHAIN A Resolution: 1.87→19.54 Å / Cor.coef. Fo:Fc: 0.9552 / Cor.coef. Fo:Fc free: 0.9425 / SU R Cruickshank DPI: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.165 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.144
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Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.279 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→19.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.95 Å / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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